This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ PrePrints) and either DOI or URL of the article must be cited.

Abstract

Understanding the genetic basis of natural phenotypic variation is of great importance, particularly since selection can act on this variation to cause evolution. We examined expression and allelic variation in candidate flowering time loci in Brassica rapa plants derived from a natural population and showing a broad range in the timing of first flowering. The loci of interest were orthologs of the Arabidopsis genes FLC and SOC1 (BrFLC and BrSOC1, respectively), which in Arabidopsis play a central role in the flowering time regulatory network, with FLC repressing and SOC1 promoting flowering. In B. rapa, there are four copies of FLC and three of SOC1. Plants were grown in controlled conditions in the lab. Comparisons were made between plants that flowered the earliest and latest, with the difference in average flowering time between these groups ~ 30 days. As expected, we found that total expression of BrSOC1 paralogs was significantly greater in early than in late flowering plants. Paralog-specific primers showed that expression was greater in early flowering plants in the BrSOC1 paralogs Br004928, Br00393 and Br009324, although the difference was not significant in Br009324. Thus expression of at least 2 of the 3 BrSOC1 orthologs is consistent with their predicted role in flowering time in this natural population. Sequences of the promoter regions of the BrSOC1 orthologs were variable, but there was no association between allelic variation at these loci and flowering time variation. For the BrFLC orthologs, expression varied over time, but did not differ between the early and late flowering plants. The coding regions, promoter regions and introns of these genes were generally invariant. Thus the BrFLC orthologs do not appear to influence flowering time in this population. Overall, the results suggest that even for a trait like flowering time that is controlled by a very well described genetic regulatory network, understanding the underlying genetic basis of natural variation in such a quantitative trait is challenging.

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Steven J Franks conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Beatriz Perez-Sweeney performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables.

Amy Litt conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Field Study Permissions

The following information was supplied relating to field study approvals (i.e., approving body and any reference numbers):

The permit is #19699-21901 from the UC Reserve System (RAMAS) for collecting seeds of Brassica rapa at the San Joaquin Marsh Reserve, the University of California, Irvine.

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

The sequences will be submitted to GenBank prior to publication.

Funding

This research was supported by grant DEB-1142784 from the National Science Foundation to S.J. Franks and funds from the Eppley Foundation for Scientific Research and The New York Botanical Garden to A. Litt. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

I wondered why you haven't presented the sequence analysis results of B. rapa SOC1 promoters in this paper. Please do include that along with the allelic variation you have pinpointed, howsoever small.

Hello Tanu Sri. Thank you for your interest and for sending your reference. We have not yet included the sequences because we are still in the process of submitting these to GenBank. Once they are submitted, the paper in PeerJ should go from a preprint to a published manuscript, and the sequences will be available. Best regards, Steve Franks

Add your feedback

Before adding feedback, consider if it can be asked as a question instead, and if so then use the Question tab. Pointing out typos is fine, but authors are encouraged to accept only substantially helpful feedback.

Follow this preprint for updates

"Following" is like subscribing to any updates related to a preprint.
These updates will appear in your home dashboard each time you visit PeerJ.

You can also choose to receive updates via daily or weekly email digests.
If you are following multiple preprints then we will send you
no more than one email per day or week based on your preferences.

Note: You are now also subscribed to the subject areas of this preprint
and will receive updates in the daily or weekly email digests if turned on.
You can add specific subject areas through your profile settings.